1)
If you are running the 16-bit timer in "free running" mode, I would recommend not to read the counter in the IC Interrupt routine but to read the input capture register in order to get the timer value at the exact time of the input capture event without any jitter.
2)
It should be no problem to work with IC and OC at the same time. Please check the sequence which you use to write to the OC-higher Byte and lower byte: first write to the HB then write to the LB. Take care also for the second IC and OC chanal which should be disabled if you don't need an interrupt on it: Access first the LB than the HB (reverse order!) => compare also to datasheet for that sequence
3)
Make sure that the OC interrupt is enabled!